DESCRIPTION: The objective of this work is to advance the state-of-the- art in electrospray/ion trap mass spectrometry of biomolecules by improving the analytical figures of merit of the instrumentation as well as by developing new experiments to gain information on high mass biologically relevant ions. The quadrupole ion trap is a remarkably powerful tool for the manipulation and mass/charge analysis of biologically-derived ions. Furthermore, it is far less expensive than other forms of instrumentation capable of performing tandem mass spectrometric experiments. The latter characteristic makes the ion trap potentially accessible to a wide range of researchers in the biomedical field. This work seeks to achieve ultra-low level analysis/detection of high mass biomolecules (low attomole levels), without preconcentration, in common analytical scenarios such as on-line capillary electrophoresis and flow injection analysis. Particular emphasis will be placed on the use of non-destructive ion detection and re-measurement within the context of multi-stage mass spectrometry experiments. The ability to store ions will be used to develop new applications for ion/molecule reactions and to explore the chemistry associated with reactions of multiply-charged biopolymers with oppositely charged ions. The ion/molecule reaction applications include a technique to increase ion currents derived from multiply-charged biopolymers by several orders of magnitude via proton transfer reactions and an approach to dealing with electrospray of mixtures involving tandem mass spectrometry and proton transfer reactions. Ion/ion reaction studies will focus on both proton transfer and electron transfer with particular attention paid to the chemistry of the odd-electron species formed via electron transfer reactions. In all cases, emphasis will be placed on experiments that can provide new information or that can enhance the performance of the ion trap over current methodology.